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Team:SJTU-Software/Database
From 2014.igem.org
3. Database
Here, we have reconstructed the database of the current existing biobricks. All the necessary information available on the Registry are collected and used to construct our own database. In this part, the source of data, the way of data collection, database structure and some facts of the biobricks in the database are introduced.
3.1.1 Data collection
Data are collected from 5 different websites on the Registry and Google Scholar.
The data needed in the reconstructed biobrick database is available from 5 sources, with four of them from the websites of Registry of Standard Biological Parts and 1 of them from Google Scholar. Addresses of those sources for BBa_B0034 are listed in Table 2.1.1, and the part name could be replaced by any biobrick.
| Name of Websites | Address |
|---|---|
| XML format | http://parts.igem.org/cgi/xml/part.cgi?part=BBa_B0034 |
| Hard information | http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_B0034 |
| Get part | http://parts.igem.org/partsdb/get_part.cgi?part=BBa_B0034 |
| Experience | http://parts.igem.org/Part:BBa_B0034:Experience |
| Google scholar | http://scholar.google.com.cn/scholar?q=BBa_B0034 |
Table 2.1.1 Sources of the data in the biobrick database, using BBa_B0034 as an example
PERL scripts are composed to connect to those links and to pick out the information we need. In order to connect to those links, we need to understand the way how biobricks on the website are named. There exist two main ways to name the biobricks, which are illustrated in Table 2.1.2 and Table 2.1.3. “BBa” is used for most biobricks, names of which consist of 3 parts. The first part is “BBa_”; the second part is a capitalized letter; the third part is several digits, the number of which depends on the previous capitalized letter (possible combinations are listed in Table 2.1.2). “pSB” is specially used for plasmids, names of which consist of 4 parts. The first part is “pSB”; the second part is one digit ranging from 1 to 9; the third part is a single pattern or a combination of two patterns listed; the fourth part can be any number from 1 to 29.
| The First Part of the Name | The Second Part of the Name | The Third Part of the Name (Number of Digits) | Examples |
|---|---|---|
| BBa_ | ||
| A | 6 | BBa_A340620 |
| B | 4 | BBa_B0034 |
| C | 4/5/6 | BBa_C0053; BBa_C10001 |
| E | 4 | BBa_E5504 |
| F | 4 | BBa_F2622 |
| G | 4/5 | BBa_G0011; BBa_G00500 |
| I | 4/5/6 | BBa_I10018 |
| J | 4/5/6 | BBa_J52100; BBa_J540013 |
| K | 6/7 | BBa_K374013; BBa_K1218016 |
| M | 4/5 | BBa_M1904; BBa_M31000 |
| P | 4 | BBa_P2007 |
| Q | 5/6 | BBa_Q200514 |
| R | 4 | BBa_R4037 |
| S | 5 | BBa_S01297 |
| T | 4 | BBa_T1009 |
| V | 4 | BBa_V1022 |
| Y | 5 | BBa_Y00100 |
| Z | 4/5 | BBa_Z0506; BBa_Z52935 |
Table 2.1.2 Rules in naming biobricks starting with “BBa_”
| The First Part of the Name | The Second Part of the Name | The Third Part of the Name | The Fourth Part of the Name | Examples |
|---|---|---|---|---|
| pSB | 1~9 | A/C/E/G/K/N/Na/R/S/St/T/Tm/Z | 1~29 | pSB1K16 |
| pSB | 1~9 | Combination of 2 letters above | 1~29 | pSB1K16 |
Table 2.1.3 Rules in naming biobricks starting with “pSB”
By substituting the names listed in Table 2.1.2 and Table 2.1.3 for the part name (BBa_B0034) in the addresses listed in Table 2.1.1, we can get access to the links about the information on biobricks. Data that are collected by PERL scripts from each website are listed in Table 2.1.4. More detailed description of those data are available in Table 2.1.5. PERL scripts used to collect those data are available on GitHub.
| Name of Websites | Address |
|---|---|
| XML format | part id; part name; part short name; part short description; part type; part status; sample status; part results; part nickname; part rating; part url; part entered; part author; Sequences; Samples; References; groups; deep subparts; specified subparts; specified subscars; features; parameters; categories; twins |
| Hard information | DNA status; Group Favorite; Whether or not deleted; Used Times; Length of Documentation |
| Get part | Confirmed Times; Not Confirmed Details |
| Experience | Average Rating; Number of Comments |
| Google scholar | Number of Publication; URL of the most related publication |
Table 2.1.4 Data collected from the 5 sources
| Property | Description |
|---|---|
| part id | Official name of the part |
| part name | BBa_B0034 |
| part short name | Part name without “BBa_” |
| part short description | The short description is usually a biological or technical descriptor of the part. It will show up on the part page |
| part type | This will state the part type/function, and will show up at the top of the part page, to the left of the DNA Status |
| part status | The status of the part based on the completeness of its documentation and characterization.system not currently in place |
| sample status | The status of the part's physical DNA (sample) in the Repository |
| part results | The experience status for a part, as documented by the part authors |
| part nickname | Nickname of the part |
| part rating | Whether there is a registry star for the part |
| part url | URL of main page for the part |
| part entered | Entered date of the part |
| part author | Author of the part |
| Sequences | Nucleotide sequence of the part |
| Samples | It’s not enabled now |
| References | It’s not enabled now |
| Groups | It’s not enabled now |
| deep subparts | All subparts that compose the subparts in the part |
| specified subparts | All subparts that compose the part |
| specified subscars | All scars between subparts |
| Features | Features of the part |
| Parameters | The parameters are submitter-decided, allowing for a degree of technical specification for the part. |
| Categories | Categories allow for a part to become content in automatically generated part tables, which is important in defining the organization of your part within the Registry, and specifically for the Catalog of Parts and Device |
| Twins | Two or more parts are twins if they have the same sequence |
| DNA status | States the DNA status of your part: Deleted, Planning, Sent, Available, etc. These statuses are generated by the Registry, so the user cannot edit them. |
| Group Favorite | One can choose if the part is a favorite of your team/group. |
| Whether or not deleted | Whether the part is deleted |
| Used Times | The number of times the part has been specified in composite parts in the Registry |
| Confirmed Times | The number of times the part sequence has been confirmed by users |
| Not Confirmed Details | Details of not confirmed facts |
| Average rating | The mean value of rating for the part given by users |
| Number of Comments | The number of comments from users |
| Number of Publication | The number of related results of the part on Google Scholar |
| URL of the most related publication | The most related result of the part on Google Scholar |
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3.1.2 Database Structure
The structure of the database is presented in Figure 3.1. The primary key in table “Main” is “part name”, with all the other tables linked to it by identical “part name”. There is no primary key in the tables except “Main” because biobricks could belong to more than one category or have more than one twins. Thus, the part name in the rest tables could be repeated for several times, depending on different biobricks.
Figure 3.1 The structure of the reconstructed biobrick database
3.1.3 Quick Facts about the Biobricks
Here are figures counting the number of the values of some important attributes judging the quality of the biobricks.
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